The England striker, whose tally of 197 goals is 52 short of Charlton's club record, has been left "angry and confused" by comments from David Moyes and chief executive Ed Woodward since the end of last season and is open to the idea of leaving Old Trafford.
But United continue to insist Rooney - named publicly by Jose Mourinho as Chelsea's sole remaining transfer target this summer - is not for sale at any price.
And Charlton, now a United director, told laureus.com: "Wayne Rooney is a Manchester United player and I think that he will continue to be a Manchester United player.
"I don't like losing really, really good players and he is a really great player.
"I was hoping one day that he might score as many goals as I had and that would have been really nice if it was at our club - and I'm still thinking that way."
Injury has kept Rooney out of United's pre-season tour of Asia and Australia and, in his absence, new signing Wilfried Zaha has caught Charlton's eye.
He said: "There's a new player, Zaha, and he's maybe been the star of the tour.
"Give him the ball and all he wants to do is beat defenders and smash it into the back of the net. I think crowds are going to love him."